Date: Thu, 23 Jan 2014 12:56:36 GMT From: pkg-fallout@FreeBSD.org To: theraven@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [REL - head-i386-default][biology/biococoa] Failed for biococoa-2.2.2 in run-depends Message-ID: <201401231256.s0NCuasg039678@beefy1.isc.freebsd.org>
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Maintainer: theraven@FreeBSD.org Last committer: theraven@FreeBSD.org Ident: $FreeBSD: head/biology/biococoa/Makefile 329819 2013-10-08 18:34:45Z theraven $ Log URL: http://beefy1.isc.freebsd.org/bulk/head-i386-default/2014-01-23_09h31m52s/logs/biococoa-2.2.2.log Build URL: http://beefy1.isc.freebsd.org/bulk/head-i386-default/2014-01-23_09h31m52s Log: ====>> Building biology/biococoa build started at Thu Jan 23 12:55:46 UTC 2014 port directory: /usr/ports/biology/biococoa building for: FreeBSD head-i386-default-job-13 11.0-CURRENT FreeBSD 11.0-CURRENT r260903 i386 maintained by: theraven@FreeBSD.org Makefile ident: $FreeBSD: head/biology/biococoa/Makefile 329819 2013-10-08 18:34:45Z theraven $ Poudriere version: 3.1-pre ---Begin Environment--- UNAME_m=i386 UNAME_p=i386 OSVERSION=1100005 UNAME_v=FreeBSD 11.0-CURRENT r260903 UNAME_r=11.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin STATUS=1 MASTERMNT=/usr/local/poudriere/data/build/head-i386-default/ref PKG_EXT=txz tpid=12556 POUDRIERE_BUILD_TYPE=bulk PKGNG=1 PKGNAME=biococoa-2.2.2 PKG_DELETE=/usr/local/sbin/pkg-static delete -y -f PKG_ADD=/usr/local/sbin/pkg-static add PWD=/root MASTERNAME=head-i386-default USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes PKG_VERSION=/poudriere/pkg-static version PKG_BIN=/usr/local/sbin/pkg-static ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- TMPDIR="/tmp" MAKE=gmake SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- TMPDIR="/tmp" "CC=/usr/bin/clang CXX=/usr/bin/clang++" SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="/usr/bin/clang" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="/usr/bin/clang-cpp" CPPFLAGS="" LDFLAGS="" CXX="/usr/bin/clang++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -o root -g wheel -m 555" BSD_INSTALL_LIB="install -s -o root -g wheel -m 444" BSD_INSTALL_SCRIPT="install -o root -g wheel -m 555" BSD_INSTALL_DATA="install -o root -g wheel -m 444" BSD_INSTALL_MAN="install -o root -g wheel -m 444" --End MAKE_ENV-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/biococoa DOCSDIR=/usr/local/share/doc/biococoa EXAMPLESDIR=/usr/local/share/examples/biococoa WWWDIR=/usr/local/www/biococoa ETCDIR=/usr/local/etc/biococoa --End SUB_LIST-- ---Begin make.conf--- ARCH=i386 MACHINE=i386 MACHINE_ARCH=i386 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /usr/local/etc/poudriere.d/make.conf #### WITH_PKGNG=yes NO_RESTRICTED=yes DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ===> Cleaning for biococoa-2.2.2 =======================<phase: check-config >============================ =========================================================================== =======================<phase: pkg-depends >============================ ===> biococoa-2.2.2 depends on file: /usr/local/sbin/pkg - not found ===> Verifying install for /usr/local/sbin/pkg in /usr/ports/ports-mgmt/pkg ===> Installing existing package /packages/All/pkg-1.2.5.txz Installing pkg-1.2.5... done If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of biococoa-2.2.2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by biococoa-2.2.2 for building =========================================================================== =======================<phase: checksum >============================ ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by biococoa-2.2.2 for building => SHA256 Checksum OK for biococoa-2.2.2-src.tgz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by biococoa-2.2.2 for building ===> Extracting for biococoa-2.2.2 => SHA256 Checksum OK for biococoa-2.2.2-src.tgz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for biococoa-2.2.2 =========================================================================== =======================<phase: build-depends >============================ ===> biococoa-2.2.2 depends on file: /usr/local/GNUstep/System/Library/Makefiles/GNUstep.sh - not found ===> Verifying install for /usr/local/GNUstep/System/Library/Makefiles/GNUstep.sh in /usr/ports/devel/gnustep-make ===> Installing existing package /packages/All/gnustep-make-2.6.6.txz Installing gnustep-make-2.6.6...Installing libobjc2-1.7_1... done done ===> Returning to build of biococoa-2.2.2 ===> biococoa-2.2.2 depends on file: /usr/local/GNUstep/System/Library/Bundles/libgnustep-cairo-024.bundle/libgnustep-cairo-024 - not found ===> Verifying install for /usr/local/GNUstep/System/Library/Bundles/libgnustep-cairo-024.bundle/libgnustep-cairo-024 in /usr/ports/x11-toolkits/gnustep-back ===> Installing existing package /packages/All/gnustep-back-0.24.0_1.txz Installing gnustep-back-0.24.0_1...Installing cairo-1.10.2_7,2...Installing xcb-util-renderutil-0.3.8...Installing libxcb-1.9.3...Installing libXau-1.0.8...Installing xproto-7.0.25... done done Installing libXdmcp-1.1.1... done Installing libpthread-stubs-0.3_4... done Installing libxml2-2.8.0_3... done done Installing xcb-util-0.3.9_1,1... done done Installing pixman-0.32.4... done Installing libXrender-0.9.8...Installing libX11-1.6.2,1...Installing kbproto-1.0.6... done done Installing renderproto-0.11.1... done done Installing fontconfig-2.11.0_1,1...Installing expat-2.1.0... done Installing freetype2-2.5.2... done Running fc-cache to build fontconfig cache... /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: caching, new cache contents: 0 fonts, 1 dirs /usr/local/lib/X11/fonts/local: caching, new cache contents: 0 fonts, 0 dirs /root/.local/share/fonts: skipping, no such directory /root/.fonts: skipping, no such directory /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: caching, new cache contents: 0 fonts, 1 dirs /root/.local/share/fonts: skipping, no such directory /root/.fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory /root/.cache/fontconfig: not cleaning non-existent cache directory /root/.fontconfig: not cleaning non-existent cache directory fc-cache: succeeded done Installing png-1.5.17... done Installing pcre-8.33... done Installing libffi-3.0.13_1... done Installing glib-2.36.3_1...Installing python27-2.7.6_1...Installing gettext-0.18.3.1... done done Installing perl5-5.16.3_6...Removing /usr/local/etc/perl5_version... Done. Creating /usr/local/etc/perl5_version... Done. Removing stale symlinks from /usr/bin... Skipping /usr/bin/perl Skipping /usr/bin/perl5 Done. Creating various symlinks in /usr/bin... Symlinking /usr/local/bin/perl5.16.3 to /usr/bin/perl Symlinking /usr/local/bin/perl5.16.3 to /usr/bin/perl5 Done. done No schema files found: doing nothing. done done Installing giflib-nox11-4.2.3... done Installing gnustep-gui-0.24.0...Installing libXt-1.1.4,1...Installing libSM-1.2.2,1...Installing libICE-1.0.8,1... done done done Installing libxslt-1.1.28_1...Installing libgpg-error-1.12... done Installing libgcrypt-1.5.3... done done Installing aspell-0.60.6.1_3... done Installing gnutls-2.12.23_3...Installing libtasn1-3.3... done Installing nettle-2.7.1...Installing gmp-5.1.3... done done Installing p11-kit-0.20.1...Installing ca_root_nss-3.15.3.1... done done done Installing cups-client-1.5.4_1... done Installing avahi-app-0.6.31...Installing dbus-glib-0.100.2...Installing dbus-1.6.18...Installing gnome_subr-1.0... done ===> Creating users and/or groups. Creating group 'messagebus' with gid '556'. Creating user 'messagebus' with uid '556'. done done Installing gdbm-1.11... done Installing gobject-introspection-1.36.0_2...Installing gnomehier-3.0... done Installing python2-2_2... done done Installing libdaemon-0.14... done <snip> Creating ../../BioCocoa.framework/Versions/2/Headers/BCSequenceStructure.h... Making build-headers for subproject BCSequence... Creating ../../BioCocoa.framework/Versions/2/Headers/BCAnnotation.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCSequence.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCSequenceArray.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCSequenceCodon.h... Making build-headers for subproject BCSequenceIO... Creating ../../BioCocoa.framework/Versions/2/Headers/BCSequenceReader.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCSequenceWriter.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCCachedSequenceFile.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCCachedFastaFile.h... Making build-headers for subproject BCSymbol... Creating ../../BioCocoa.framework/Versions/2/Headers/BCAminoAcid.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCNucleotide.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCSymbol.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCNucleotideDNA.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCNucleotideRNA.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCSymbolSet.h... Making build-headers for subproject BCTools... Creating ../../BioCocoa.framework/Versions/2/Headers/BCSequenceTool.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCToolDigest.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCToolHydropathyCalculator.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCToolMassCalculator.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCToolComplement.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCToolSequenceFinder.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCToolSymbolCounter.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCToolTranslator.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCToolTranslatorDNA.h... Making build-headers for subproject BCUtils... Creating ../../BioCocoa.framework/Versions/2/Headers/BCDataMatrix.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCUtilData.h... Creating ../../BioCocoa.framework/Versions/2/Headers/BCUtilStrings.h... Making build-headers for subproject BCFoundation... Creating ../BioCocoa.framework/Versions/2/Headers/BCFoundation.h... Creating ../BioCocoa.framework/Versions/2/Headers/BCFoundationDefines.h... Creating ../BioCocoa.framework/Versions/2/Headers/BCStringDefinitions.h... Creating ../BioCocoa.framework/Versions/2/Headers/BCPreferences.h... Making build-headers for framework BioCocoa... Creating derived_src/.stamp... Creating BioCocoa.framework/Versions/2/Resources... Updating Version/Current symlink... Making all in subprojects of framework BioCocoa... Making all in subprojects of subproject BCFoundation... Making all for subproject BCAlignment... Compiling file BCPairwiseAlignment.m ... Compiling file BCScoreMatrix.m ... Compiling file BCSequenceAlignment.m ... Linking subproject BCAlignment ... clang: warning: argument unused during compilation: '-pthread' Making all for subproject BCAnalysis... Compiling file BCMCP.m ... Compiling file BCSuffixArray.m ... Linking subproject BCAnalysis ... clang: warning: argument unused during compilation: '-pthread' Making all for subproject BCGeneExpression... Compiling file BCSeries.m ... Compiling file BCSample.m ... Compiling file BCPlatform.m ... Compiling file BCParseSOFT.m ... Linking subproject BCGeneExpression ... clang: warning: argument unused during compilation: '-pthread' Making all for subproject BCGeneticCode... Compiling file BCCodonDNA.m ... Compiling file BCCodon.m ... Compiling file BCCodonRNA.m ... Compiling file BCGeneticCode.m ... Linking subproject BCGeneticCode ... clang: warning: argument unused during compilation: '-pthread' Making all for subproject BCProteinStructure... Compiling file BCAtom.m ... Compiling file BCProteinStructure.m ... Compiling file BCSecondaryStructure.m ... Compiling file BCChain.m ... Compiling file BCResidue.m ... Compiling file BCSequenceStructure.m ... Linking subproject BCProteinStructure ... clang: warning: argument unused during compilation: '-pthread' Making all for subproject BCSequence... Compiling file BCAnnotation.m ... Compiling file BCSequence.m ... Compiling file BCSequenceArray.m ... Compiling file BCSequenceCodon.m ... Linking subproject BCSequence ... clang: warning: argument unused during compilation: '-pthread' Making all for subproject BCSequenceIO... Compiling file BCSequenceReader.m ... BCSequenceReader.m:167:63: warning: instance method '-initWithRTF:documentAttributes:' not found (return type defaults to 'id') [-Wobjc-method-access] NSAttributedString *rtfstring = [[NSAttributedString alloc] initWithRTF: [entryString dataUsingEncoding: NSUTF8StringEncoding] documentAttributes: nil]; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BCSequenceReader.m:798:48: warning: incompatible pointer types sending 'id' to parameter of type 'NSString **' [-Wincompatible-pointer-types] [lineScanner scanUpToString:@" " intoString: nil]; ^~~ /usr/local/include/objc/runtime.h:207:14: note: expanded from macro 'nil' # define nil ((id)_OBJC_NULL_PTR) ^~~~~~~~~~~~~~~~~~~~ /usr/local/GNUstep/System/Library/Headers/Foundation/NSScanner.h:102:68: note: passing argument to parameter 'value' here - (BOOL) scanUpToString: (NSString*)string intoString: (NSString**)value; ^ BCSequenceReader.m:830:12: warning: using 'stringWithString:' with a literal is redundant [-Wobjc-redundant-literal-use] name = [NSString stringWithString: @"alignment"]; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3 warnings generated. Compiling file BCSequenceWriter.m ... Compiling file BCCachedSequenceFile.m ... Compiling file BCCachedFastaFile.m ... BCCachedFastaFile.m:126:71: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] NSLog(@"Attempting to read past end of forward stand: (%lu)\n", aPos); ~~~ ^~~~ %llu BCCachedFastaFile.m:132:16: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if (newPos < 0) { ~~~~~~ ^ ~ BCCachedFastaFile.m:133:72: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat] NSLog(@"Attempting to read past end of reverse strand: (%lu)\n", aPos); ~~~ ^~~~ %llu 3 warnings generated. Linking subproject BCSequenceIO ... clang: warning: argument unused during compilation: '-pthread' Making all for subproject BCSymbol... Compiling file BCAminoAcid.m ... Compiling file BCNucleotide.m ... Compiling file BCSymbol.m ... Compiling file BCNucleotideDNA.m ... BCNucleotideDNA.m:445:43: warning: 'BCNucleotideDNA' may not respond to 'initWithDictionary:' aBase = [[[BCNucleotideDNA alloc] initWithDictionary: aBase] autorelease]; ~~~~~~~~~~~~~~~~~~~~~~~ ^ 1 warning generated. Compiling file BCNucleotideRNA.m ... BCNucleotideRNA.m:454:43: warning: 'BCNucleotideRNA' may not respond to 'initWithDictionary:' aBase = [[[BCNucleotideRNA alloc] initWithDictionary: aBase] autorelease]; ~~~~~~~~~~~~~~~~~~~~~~~ ^ 1 warning generated. Compiling file BCSymbolSet.m ... Linking subproject BCSymbol ... clang: warning: argument unused during compilation: '-pthread' Making all for subproject BCTools... Compiling file BCSequenceTool.m ... Compiling file BCToolDigest.m ... Compiling file BCToolHydropathyCalculator.m ... Compiling file BCToolMassCalculator.m ... Compiling file BCToolComplement.m ... Compiling file BCToolSequenceFinder.m ... Compiling file BCToolSymbolCounter.m ... Compiling file BCToolTranslator.m ... Compiling file BCToolTranslatorDNA.m ... Linking subproject BCTools ... clang: warning: argument unused during compilation: '-pthread' Making all for subproject BCUtils... Compiling file BCDataMatrix.m ... Compiling file BCUtilData.m ... Compiling file BCUtilStrings.m ... BCUtilStrings.m:98:23: warning: incompatible pointer types sending 'id' to parameter of type 'int *' [-Wincompatible-pointer-types] if ([scanner scanInt:nil]) ^~~ /usr/local/include/objc/runtime.h:207:14: note: expanded from macro 'nil' # define nil ((id)_OBJC_NULL_PTR) ^~~~~~~~~~~~~~~~~~~~ /usr/local/GNUstep/System/Library/Headers/Foundation/NSScanner.h:94:25: note: passing argument to parameter 'value' here - (BOOL) scanInt: (int*)value; ^ BCUtilStrings.m:100:24: warning: incompatible pointer types sending 'id' to parameter of type 'int *' [-Wincompatible-pointer-types] if ([scanner scanInt:nil]) ^~~ /usr/local/include/objc/runtime.h:207:14: note: expanded from macro 'nil' # define nil ((id)_OBJC_NULL_PTR) ^~~~~~~~~~~~~~~~~~~~ /usr/local/GNUstep/System/Library/Headers/Foundation/NSScanner.h:94:25: note: passing argument to parameter 'value' here - (BOOL) scanInt: (int*)value; ^ 2 warnings generated. Linking subproject BCUtils ... clang: warning: argument unused during compilation: '-pthread' Making all for subproject BCFoundation... Compiling file BCStringDefinitions.m ... Compiling file BCPreferences.m ... Linking subproject BCFoundation ... clang: warning: argument unused during compilation: '-pthread' Making all for framework BioCocoa... Creating derived_src/NSFramework_BioCocoa.m... Compiling file derived_src/NSFramework_BioCocoa.m ... Linking framework BioCocoa ... Copying resources into the framework wrapper... Copying resources from subprojects into the framework wrapper... Creating BioCocoa.framework/Versions/2/Resources/Info-gnustep.plist... gmake[1]: Leaving directory `/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2' =========================================================================== =======================<phase: run-depends >============================ ===> biococoa-2.2.2 depends on file: /usr/local/GNUstep/System/Library/Makefiles/GNUstep.sh - found ===> biococoa-2.2.2 depends on file: /usr/local/GNUstep/System/Library/Bundles/libgnustep-cairo-024.bundle/libgnustep-cairo-024 - not found ===> Verifying install for /usr/local/GNUstep/System/Library/Bundles/libgnustep-cairo-024.bundle/libgnustep-cairo-024 in /usr/ports/x11-toolkits/gnustep-back ===> Installing existing package /packages/All/gnustep-back-0.24.0_1.txz Installing gnustep-back-0.24.0_1...gnustep-back-0.24.0_1 already installed Failed to install the following 1 package(s): /packages/All/gnustep-back-0.24.0_1.txz *** Error code 70 Stop. make: stopped in /usr/ports/biology/biococoa ===> Cleaning for biococoa-2.2.2
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